compilation instructions

You need to download FSL from source (no need to install) and add the follow to your .bash_profile

export FSLDIR=<path to your extracted fsl>
. ${FSLDIR}/etc/fslconf/fsl.sh

You also need to add 

export FSLDEVDIR=<folder where includes and libraries will go>

Then create $FSLDEVDIR and associated folders:
mkdir -p  $FSLDEVDIR  $FSLDEVDIR/extras $FSLDEVDIR/extras/include $FSLDEVDIR/extras/src

Copy/move the folder extras/ELC1.04/ELC from this repository to your extras/ELC1.04/ELC
Copy $FSLDIR/src/FastPDlib to $FSLDEVDIR/extras/src

Then compile (make install) each repository directory in order (note you require c++11 support):

newmesh
DiscreteOpt
FastPDlib (from $FSLDEVDIR/extras/src)
MSMRegLib
MSM

Binaries will be deposited in the MSM folder